"""
Specifically, among the genes with expression values in the interquartile range, we identified the 1,000 genes that have the most-conserved ranks among samples and assessed their median expression levels in each sample. We then derived scaling factors that adjust these medians to a common value. Finally, these factors were used to scale expression values of all genes in the samples.
"""

Some unclear points to me:

Is it a procedure similar to the DESeq scaling factor computation?

they have expression for different tissues in different species, are they computing the scaling factor per species (pulling the samples of the different tissues from the same specie) or pulling all the samples together?

what about replicates? Are they also pulled with the others or a first normalization is made between replicates?

in a more general way, is someone know a classical protocol to normalize samples between species?